Halibut mitochondrial genomes contain extensive heteroplasmic tandem repeat arrays involved in DNA recombination

BMC Genomics

Table 2 Estimates of gene specific variation related to the mitochondrial ribosomal DNA gene region

Gene ¹	Halibuts; within-species ²		Halibuts; between-species ³		Theragra; within-species ⁴
	Observed	Relative	Observed	Relative	Observed	Relative
ND1	0.0079	4.4	0.186	4.0	0.0226	4.6
ND2	0.0080	4.4	0.216	4.6	0.0163	3.3
ND3	0.0029	1.6	0.189	4.0	0.0172	3.5
ND4L	0.0090	5.0	0.128	2.7	0.0034	0.7
ND4	0.0051	2.8	0.199	4.2	0.0167	3.4
ND5	0.0067	3.7	0.209	4.4	0.0207	4.2
N6	0.0077	4.3	0.201	4.3	0.0172	3.5
COI	0.0045	2.5	0.151	3.2	0.0109	2.2
COII	0.0039	2.2	0.152	3.2	0.0043	0.9
COIII	0.0034	1.9	0.144	3.1	0.0140	2.9
A6	0.0068	3.8	0.198	4.2	0.0161	3.3
A8	0.0040	2.2	0.137	2.9	0.0119	2.4
Cyt B	0.0067	3.7	0.193	4.1	0.0158	3.2
CR ⁵	0.0211	11.7	0.220	4.7	0.0160	3.3
tRNA	0.0028	1.6	0.062	1.3	0.0013	0.3
SSU	0.0014	0.8	0.042	0.9	0.0063	1.3
LSU	0.0019	1.1	0.050	1.1	0.0041	0.8
SSU + LSU	0.0018	1.0	0.047	1.0	0.0049	1.0

Notes: ¹ Protein genes – all gene positions except stop codons. The variable sites are mainly transition substitutions at third codon positions. CR – control region nucleotides including the first and last three motifs of tandem repeates. tRNA genes – pool of all 22 tRNA genes, ca 1550 bp; SSU + LSU – combined mitochondrial small and large ribosomal subunit RNA genes, ca 2665 bp.
² Estimated avarage values within the three halibut species (Atlantic-, Pacific-, and Greenland halibuts) based on four specimens of each. The observed variation value is number of variable sites divided on total number of nucleotides of that particular mitochondrial region. The relative variation value is the observed variation divided on the combined SSU/LSU variation.
³ Estimated nucleotide variation between halibut species and includes the Atlantic halibut (Hh-1 specimen), Pacific halibut (Hs-1 specimen), Greenland halibut (Rh-1 specimen), Spotted halibut, and Barfin flounder. Key features of species are given in Table 1.
⁴ Estimated nucleotide variation within pollocks (Theragra; Gadidae) and is based on 12 specimens representing one single species [11, 12].
⁵ The elevated substitution level in CR within halibut species is boxed.

ISSN: 1471-2164